In co-operation with scientists and engineers from the Technical University Ilmenau and the Institute for Physical High Technology Jena a novel system for the automated handling of magnetic beads was developed. The beads with diameters of 400...800 µm are in micro plates with up to 1.536 wells or in special nano plates with up to 3.456 wells. The system gives the possibility to transfer beads separately and selective from one plate to another, but also to transfer all beads simultaneously from one plate to another within some seconds.